8F5A: KS1 TCR

Crystal Structure of KS1 TCR in complex with HLA-B*57:01-TW10. Determined by X-ray diffraction at 1.95 Å resolution. Released 22 May 2024.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 5
Atoms: 7,086
Mol. weight: 94.47 kDa
Released: 22 May 2024

Explore 8F5A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F5A contains 25 α-helices and 71 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
α-helix	90	1
β-strand	91-94	4	7

Chain C: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	30-38	9	9
β-strand	44-50	7	9
β-strand	57-59	3	8
β-strand	62-67	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-94	9	9
β-strand	103-104	2	9
β-strand	108-113	6	9
β-strand	122-126	5	10
β-strand	135-140	6	10
α-helix	149-151	3
β-strand	156-158	3	10
α-helix	159-161	3
β-strand	162-166	5	10
α-helix	167-169	3
β-strand	171-180	10	10
α-helix	187-190	4
β-strand	201	1	10

Chain D: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-24	6	11
α-helix	25	1
β-strand	31-38	8	12
β-strand	42-50	9	12
β-strand	53-57	5	12
β-strand	65-69	5	11
β-strand	75-79	5	11
α-helix	84-86	3
β-strand	88-95	8	12
β-strand	102-103	2	12
β-strand	107-112	6	12
α-helix	115-117	3
β-strand	119	1	13
β-strand	122-126	5	14
α-helix	127-129	3
α-helix	130-136	7
β-strand	138-148	11	14
β-strand	149	1	13
β-strand	153-159	7	15
β-strand	162-164	3	15
β-strand	168-170	3	14
α-helix	174	1
β-strand	175-176	2	14
β-strand	186-195	10	14
α-helix	196-199	4
β-strand	205-212	8	15
β-strand	215	1	16
α-helix	226-227	2
β-strand	229	1	16
β-strand	231-238	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
heavy chain HLA-B*57:01	A	protein	278	Homo sapiens	U6BR87 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
KS1 TCR alpha chain	C	protein	208	Homo sapiens
KS1 TCR beta chain	D	protein	239	Homo sapiens
TW10 peptide	E	protein	10	Human immunodeficiency virus 1	P04585 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8F5A_1 heavy chain HLA-B*57:01 (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRMAPRAPWIEQEGPEYW
DGETRNMKASAQTYRENLRIALRYYNQSEAGSHIIQVMYGCDVGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSS

Sequence of entity 2 (B), FASTA

>8F5A_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>8F5A_3 KS1 TCR alpha chain (chains C)
KQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSG
RLNASLDKSSGRSTLYIAASQPGDSATYLCAVTLNNNAGNMLTFGGGTRLMVKPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D), FASTA

>8F5A_4 KS1 TCR beta chain (chains D)
GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPG
RFSGRQFSNSRSEMNVSTLELGDSALYLCASSVGGTEAFFGQGTRLTVVEDLKNVFPPEV
AVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALND
SRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Sequence of entity 5 (E), FASTA

>8F5A_5 TW10 peptide (chains E)
TSTLQEQIGW

Primary citation

Public T cell clonotypes are selected in HLA-B ∗ 57:01 + /HIV + patients independently of the viral load. Chatzileontiadou, D.S.M., Lobos, C.A., Robson, H. et al. Cell Rep (2024) 43:114555-114555. DOI 10.1016/j.celrep.2024.114555 · PubMed

Other PDB entries of the same protein (UniProt U6BR87 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6V2O 1.27 Å, HLA-B*57:01 presenting the peptide ASLNLPAVSW
7R7Y 1.6 Å, Crystal structure of HLA-B*5701 complex with an HIV-1 Gag-derived epitope QW9 S3T variant
8F7M 1.88 Å, Crystal Structure of HLA-B*57:01-TW10-T242N complex
7R7X 2.1 Å, Crystal structure of HLA-B*5701 complex with an HIV-1 Gag-derived epitope QW9

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